X-ray structure of oxalyl-CoA decarboxylase in complex with formyl-CoA

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).

Ligands and binding sites

• TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
• ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
• FYN · S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-9,13,15-trihydroxy-10,10-dimethyl-13,15-dioxido-4,8-dioxo-12,14,16-trioxa-3,7-diaza-13,15-diphosphaheptadec-1-yl} thioformate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• PGE · Triethylene glycol · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 3756 Ų buried · 45 hydrogen bonds · protein-protein

Compared structures

• 2JI8 · X-ray structure of Oxalyl-CoA decarboxylase in complex with Formyl- CoA · the same entry in another collection · chain A against A, TM-score 1.00
• P40149 · AlphaFold monomer V2.0 prediction for oxalyl-CoA decarboxylase (P40149) · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P40149
• Elsewhere: RCSB PDB 2JI8 · PDBe 2JI8 · UniProt P40149